Source code for galaxy.workflow.trs_proxy

import logging
import os
import re
import urllib.parse
from typing import List

import yaml

from galaxy.config import Configuration
from galaxy.exceptions import (
    MessageException,
    RequestParameterInvalidException,
)
from galaxy.files.uris import validate_non_local
from galaxy.util import (
    asbool,
    DEFAULT_SOCKET_TIMEOUT,
    requests,
)
from galaxy.util.config_parsers import IpAllowedListEntryT
from galaxy.util.search import parse_filters

log = logging.getLogger(__name__)

# Make configurable via YAML,JSON
DEFAULT_TRS_SERVERS = [
    {
        "id": "dockstore",
        "api_url": "https://dockstore.org/api",
        "link_url": "https://dockstore.org",
        "label": "Dockstore",
        "doc": "Dockstore is an open platform used by the GA4GH for sharing Docker-based tools and workflows.",
    },
]
GA4GH_GALAXY_DESCRIPTOR = "GALAXY"
TRS_URL_REGEX = (
    r"(?P<trs_base_url>https?:\/\/.+)\/ga4gh\/trs\/v2\/tools\/(?P<tool_id>.+)\/versions\/(?P<version_id>[^\/]+).*"
)


[docs]def parse_search_kwds(search_query):
    filters = {
        "organization": "organization",
        "o": "organization",
        "name": "name",
        "n": "name",
    }
    keyed_terms, description_term = parse_filters(search_query, filters)
    query_kwd = {
        "toolClass": "Workflow",
        "descriptorType": "GALAXY",
    }
    if description_term and description_term.strip():
        query_kwd["description"] = (description_term,)

    if keyed_terms is not None:
        for key, value, _ in keyed_terms:
            query_kwd[key] = value
    return query_kwd


[docs]class TrsProxy:
[docs]    def __init__(self, config: Configuration):
        config_file = config.trs_servers_config_file
        if config_file and os.path.exists(config_file):
            with open(config_file) as f:
                server_list = yaml.safe_load(f)
        else:
            server_list = DEFAULT_TRS_SERVERS
        self._server_list = server_list if server_list else []
        self._server_dict = {t["id"]: t for t in self._server_list}
        self.fetch_url_allowlist_ips = config.fetch_url_allowlist_ips

[docs]    def get_servers(self):
        return self._server_list

[docs]    def get_server(self, trs_server):
        trs_url = self._server_dict[trs_server]["api_url"]
        return TrsServer(trs_url)

[docs]    def server_from_url(self, trs_url):
        return TrsServer(trs_url)

[docs]    def get_trs_id_and_version_from_trs_url(self, trs_url):
        parts = self.match_url(trs_url, self.fetch_url_allowlist_ips)
        if parts:
            return self.server_from_url(parts["trs_base_url"]), parts["tool_id"], parts["version_id"]
        raise RequestParameterInvalidException(f"Invalid TRS URL {trs_url}.")

[docs]    def get_version_from_trs_url(self, trs_url):
        server, trs_tool_id, trs_version_id = self.get_trs_id_and_version_from_trs_url(trs_url=trs_url)
        return server.get_version_descriptor(trs_tool_id, trs_version_id)

[docs]    def match_url(self, url, ip_allowlist: List[IpAllowedListEntryT]):
        if url.lstrip().startswith("file://"):
            # requests doesn't know what to do with file:// anyway, but just in case we swap
            # out the implementation
            raise RequestParameterInvalidException("Invalid TRS URL %s", url)
        validate_non_local(url, ip_allowlist=ip_allowlist or [])
        return self._match_url(url)

    def _match_url(self, url):
        if matches := re.match(TRS_URL_REGEX, url):
            match_dict = matches.groupdict()
            match_dict["tool_id"] = urllib.parse.unquote(match_dict["tool_id"])
            return match_dict
        else:
            return None


[docs]class TrsServer:
[docs]    def __init__(self, trs_url):
        self._trs_url = trs_url

[docs]    def get_tools(self, **kwd):
        query_kwd = {}
        for key in ["toolClass", "descriptorType", "description", "name", "organization"]:
            value = kwd.pop(key, None)
            if value is not None:
                query_kwd[key] = value

        trs_api_url = self._get_api_endpoint(**kwd)
        return self._get(trs_api_url, params=query_kwd)

[docs]    def get_tool(self, tool_id, **kwd):
        trs_api_url = self._get_tool_api_endpoint(tool_id, **kwd)
        return self._get(trs_api_url)

[docs]    def get_versions(self, tool_id, **kwd):
        trs_api_url = f"{self._get_tool_api_endpoint(tool_id, **kwd)}/versions"
        return self._get(trs_api_url)

[docs]    def get_version(self, tool_id, version_id, **kwd):
        trs_api_url = f"{self._get_tool_api_endpoint(tool_id, **kwd)}/versions/{version_id}"
        return self._get(trs_api_url)

[docs]    def get_version_descriptor(self, tool_id, version_id, **kwd):
        trs_api_url = (
            f"{self._get_tool_api_endpoint(tool_id, **kwd)}/versions/{version_id}/{GA4GH_GALAXY_DESCRIPTOR}/descriptor"
        )
        return self._get(trs_api_url)["content"]

[docs]    def get_trs_url(self, tool_id: str, version_id: str):
        return f"{self._get_tool_api_endpoint(tool_id)}/versions/{version_id}"

    def _quote(self, tool_id, **kwd):
        if asbool(kwd.get("tool_id_b64_encoded", False)):
            import base64

            tool_id = base64.b64decode(tool_id)
        tool_id = urllib.parse.quote_plus(tool_id)
        return tool_id

    def _get(self, url, params=None):
        response = requests.get(url, params=params, timeout=DEFAULT_SOCKET_TIMEOUT)
        if response.ok:
            return response.json()
        else:
            code = response.status_code
            message = response.text
            try:
                trs_error_dict = response.json()
                code = int(trs_error_dict["code"])
                message = trs_error_dict["message"]
            except Exception:
                pass
            raise MessageException.from_code(code, message)

    def _get_api_endpoint(self, **kwd):
        trs_url = self._trs_url
        trs_api_endpoint = f"{trs_url}/ga4gh/trs/v2/tools"
        return trs_api_endpoint

    def _get_tool_api_endpoint(self, tool_id, **kwd):
        tool_id = self._quote(tool_id, **kwd)
        trs_api_url = f"{self._get_api_endpoint(**kwd)}/{tool_id}"
        return trs_api_url